So I've installed a significant number of mods using MO2 and done the whole process of clearing all the issues from the plugins, and when I run Skyrim through SKSE the game runs... But one of my 163 mods are there. It is giving me the following error first:

"A DLL plugin has failed to load correctly. If a new verson of skyrim was just released, the plugin needs to be updated. Please check the mod's webpage for updates."

Which lists the following mods as being disabled due to compatibility issues:

Exended Hotkey System.dll
fiss.dll
Fuz Ro D'oh.dll
gotobed.dll
hdtHighHeelNative.dll
hdtSMP64.dll
Jcontainers64.dll
PapyrusUtil.dll
showRaceMenu_preCacheKiller.dll


Then it just loads straight into the base game, with me on the wagon. Installed content shows me the Creation Club content is all installed just fine, but none of my mods are working. I don't even have an option ingame to see the mod list. Is there something I'm missing?

That's exactly what it sounds like, all .dll listed are incompatible with your game version (GOG 1.6.659).
Look on their respective pages if they have a GOG version available, otherwise you are out of luck.

Fuz Ro Doh and JContainers: neither authors intends to make a GOG version, but both mods are open source and it is possible to ask someone else with knowledge to update them.

PapyrusUtil author said he'll check it out eventually, but it's not a priority.
Faster HDT-SMP (hdtSMP64.dll) - author also said something similar. ^

I don't know the others.

Well I've removed or updated all the ones on the list and the game's still not showing any mods and just starting at the wagon. Is there something else I have to do?

NO, they dot appear! I have installed SKYUI, SKSE64 for GOG and a Matter of Time, and there is no way to specify to the Game that the mods are to be used ... Standard Skyrim loader has a button to select the mods to add to the game. Skyrim SE or AE loader does not have that facility !

What can we add our mods! Under Windows/10 you can use Vortex to load your mods, because I am on Linux/Wine and that program does not work under Wine !

I figured out the problem! Even with the patch to SKSE, it's not loading mods unless I copy the mod text file from my app local folder and stick it in the proper directory. Apparently I'll have to do this every time I change a mod too, which kinda sucks. But hey, I got it working.

Did you get the GOG version of game_skyrimse.dll for MO2?
https://www.nexusmods.com/skyrimspecialedition/mods/6194?tab=files

I'm only using a single mod under Wine/Linux, the Unofficial Skyrim Special Edition Patch. I tried a few of the mod managers and couldn't seem to get it working either, until I found this file (referenced from within the wine prefix):

C:\Users\your_id\AppData\Local\Skyrim Special Edition GOG\plugins.txt

In there the patch was referenced and I just had to put an asterisk at the beginning of the line to enable it:

*Unofficial Skyrim Special Edition Patch.esp

I don't know if this file existed before I messed with MO2 or not.

This is what I have been asking about in my thread:
https://www.gog.com/forum/elder_scrolls_series/mo2_and_appdatalocal_possible_solve

Feel free to discuss if the MO2 "fix", actually solves the problwm or if my work around solves it. Would be great to have the information for everyone to learn about until a resolution presents itself.

What I said about Vortex works only with the STEAM version of Skyrim SE or AE. The GOG version CANNOT use any MODS!

It's a rip off! It's like ordering a Winter Leather Coat and when you receive it and try it you discover that it is not true leather and there is nothing inside lining with the coat!

I am very disappointed that this is the state of things. Usually GOG provides a patched version of the Steam version as demonstrated by a dummy presence of steamapi.dll in the games such as The Witcher 2&3, all Spellforce games, Solosta, Kingdoms of Amalur re-reconning and many others.

Just as a note: I do own the license of the Steam version of Skyrim SE, but as usual, when a Steam game appears on GOG, I always buy it because I so not like to have to be online to play my games (The same reason I do not use Galaxy, not even to get updates!)

Vortex was the first tool to receive official support for Skyrim-GOG... what do you mean it doesn't work? there are several users recommending it over MO2 (it took a few days until MO2 got its GOG update).
Maybe having Skyrim-Steam installed simultaneously is making your Vortex act weird, if that's the case, you can try to report it on Nexus/Vortex Discord, surely some more experienced user will try to help you.

@GrandBreaker
It looks like ExtendedHotkeySystem.dll got a new update a few hours ago.

Late reply, yeah I did. I'm still having to do this thing with the txt file, but I have gotten it working. Outside of a handful of mods that the dll file still doesn't function right, like HDT-SMP.
Uh. It is working. And if we're being honest, Gogrim is going to be the most friendly to modders since it's DRM free and therefor steam/bethesda can't break things with auto updates or always connected BS.

Uh; not working at all for me. Can't believe how 8up this GoG version of Skyrim is for mods. Without mods it's basically nan elder scrolls game at all.

I also don't know how to activate the mods.

I got Skyrim Special Edition on GOG (without Galaxy) and I have installed a few mods manually (without Vortex or similar software), I believe I did that manual installation correctly, but the mods are absent when I start playing.

I chose some standalone mods exactly because I wanted to keep things simple, and avoid those that have more complex requirements, like those that need SKSE and multiple other files.

Like another user said: "Standard Skyrim loader has a button to select the mods to add to the game. Skyrim SE or AE loader does not have that", so how can I enable the mods? Maybe it's as simple as writing or editing a small text file. Again, I am not using any mod organizer software, so the procedure might be different from the standard one for GOG gamers.

Does anyone know?

Yes it is.
In C:\Users\Username\AppData\Local\Skyrim Special Edition GOG make a text file and name it plugins.txt
Write the mods in the order you want them to load. ESM's first.
An * at the beginning means it is enabled (removing the * disables the mod.
See the attached pic for my example.